--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halUpdateBranchLengths.xml	Fri Feb 06 10:39:02 2026 +0000
@@ -0,0 +1,50 @@
+<tool id="hal_halupdatebranchlengths" name="halUpdateBranchLengths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>updates the branch lengths of a tree</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## Copy input HAL to ensure that it is not modified.
+        cp '$input_hal' writable_hal.hal && 
+        halUpdateBranchLengths
+            writable_hal.hal '$newickTree' &&
+        ## echo 'ok' to check it with assert_stdout. This is needed because there is no other stdout output, 
+        ## and the output HAL file checksum always changes even with identical inputs.
+        echo 'ok'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <param name="newickTree" type="text" value="" label="Newick Tree" help="Newick tree (must be identical, except for the branch lengths)">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_newick"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="hal" label="${tool.name} on ${on_string}" from_work_dir="writable_hal.hal"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="newickTree" value="(Genome_1:2,Genome_2:2,Genome_3:1)Genome_0;"/>
+            <output name="out_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="50000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="ok"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help><![CDATA[
+halUpdateBranchLengths updates the branch lengths stored in a HAL alignment using values provided by a given external Newick tree. 
+The topology of the Newick tree must exactly match the topology of the tree already stored in the HAL file. 
+Only branch lengths are replaced.
+
+A new HAL file is created as output instead of modifying the input HAL file.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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